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LOC130066698 ATAC-STARR-seq lymphoblastoid active region 18477 [ Homo sapiens (human) ]

Gene ID: 130066698, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066698
Gene description
ATAC-STARR-seq lymphoblastoid active region 18477
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC130066698 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (41425906..41426345)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (39814561..39815000)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (42797833..42798272)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene FAM3 metabolism regulating signaling molecule B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18470 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr21:42731293-42732096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42739613-42740114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42740714-42741402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42741403-42742089 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 21:42745414 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 21:42746568 and 21:42746578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42750497-42750998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42750999-42751498 Neighboring gene MX dynamin like GTPase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18479 Neighboring gene MX dynamin like GTPase 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:42824122-42825321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42830117-42830618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42851654-42852154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42852155-42852655 Neighboring gene transmembrane serine protease 2 Neighboring gene transmembrane protease serine 2 breakpoint cluster recombination region Neighboring gene TMPRSS2 promoter region Neighboring gene TMPRSS2 repressive element NBS1 Neighboring gene TMPRSS2 repressive element NBS2 Neighboring gene TMPRSS2 repressive element NBS4 Neighboring gene TMPRSS2 androgen receptor-responsive -13 kb enhancer Neighboring gene TMPRSS2 -17 kb enhancer Neighboring gene TMPRSS2 E3 enhancer Neighboring gene uncharacterized LOC124905021

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_201114.1 

    Range
    101..540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    41425906..41426345
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    39814561..39815000
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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